Structure of PDB 4dpd Chain A Binding Site BS02

Receptor Information
>4dpd Chain A (length=530) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMEQVCDVFDIYAICACCKVEEVFNNYTFRGLGNKGVLPWKCNSLDMKYF
CAVTTYVNESKYEKLKYKRCKYLNKKLQNVVVMGRTSWESIPKKFKPLSN
RINVILSRTLKKEDFDEDVYIINKVEDLIVLLGKLNYYKCFIIGGSVVYQ
EFLEKKLIKKIYFTRINSTYECDVFFPEINENEYQIISVSDVYTSNNTTL
DFIIYKKTDEEEDDFVYFNFNKEKEEKNKNSIHPNDFQIYNSLKYKYHPE
YQYLNIIYDIMMNGNKQSDRTGVGVLSKFGYIMKFDLSQYFPLLTTKKLF
LRGIIEELLWFIRGETNGNTLLNKNVRIWEANGTREFLDNRKLFHREVND
LGPIYGFQWRHFGAEYTNMYDNYENKGVDQLKNIINLIKNDPTSRRILLC
AWNVKDLDQMALPPCHILCQFYVFDGKLSCIMYQRSCDLGLGVPFNIASY
SIFTHMIAQVCNLQPAQFIHVLGNAHVYNNHIDSLKIQLNRIPYPFPTLK
LNPDIKNIEDFTISDFTIQNYVHHEKISMD
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain4dpd Chain A Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4dpd Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target
Resolution2.5 Å
Binding residue
(original residue number in PDB)		C15 A16 L40 G44 V45 G105 R106 T107 S108 L127 S128 R129 T130 N144 I164 G166 S167 V168 V169 E172
Binding residue
(residue number reindexed from 1)		C15 A16 L32 G36 V37 G84 R85 T86 S87 L106 S107 R108 T109 N123 I143 G145 S146 V147 V148 E151
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) L46 D54 E382 W404 Y430 C490 R510 D513
Catalytic site (residue number reindexed from 1) L38 D46 E307 W329 Y355 C415 R435 D438
Enzyme Commision number 1.5.1.3: dihydrofolate reductase.
2.1.1.45: thymidylate synthase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004146 dihydrofolate reductase activity
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016491 oxidoreductase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0006730 one-carbon metabolic process
GO:0009165 nucleotide biosynthetic process
GO:0032259 methylation
GO:0046654 tetrahydrofolate biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4dpd, PDBe:4dpd, PDBj:4dpd
PDBsum4dpd
PubMed23035243
UniProtA7UD81

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